Power-Law Signatures and Patchiness in Genechip Oligonucleotide Microarrays

Genechip oligonucleotide microarrays have been used widely for transcriptional profiling of a large number of genes in a given paradigm. Gene expression estimation precedes biological inference and is given as a complex combination of atomic entities on the array called probes. These probe intensities are further classified into perfect-match (PM) and mismatch (MM) probes. While former is a measure of specific binding, the latter is a measure of non-specific binding. The behavior of the MM probes has especially proven to be elusive. The present study investigates qualitative similarities in the distributional signatures and local correlation structures/patchiness between the PM and MM probe intensities. These qualitative similarities are established on publicly available microarrays generated across laboratories investigating the same paradigm. Persistence of these similarities across raw as well as background subtracted probe intensities is also investigated. The results presented raise fundamental concerns in interpreting Genechip oligonucleotide microarray data.